[gmx-users] output unimaged trajectory?

[Nuno R. L. Ferreira]

----- Original Message ----- 
From: <david.evans at ulsop.ac.uk>
To: "Nuno R. L. Ferreira list for GROMACS users" <gmx-users at gromacs.org>
Sent: Tuesday, July 13, 2004 5:02 PM
Subject: Re: [gmx-users] output unimaged trajectory?


Thanks for the reply. I've been playing with trjconv for a while now,
and I can get it to keep my central (DNA) molecule together, with the
-pbc nojump option. It seems to drift slowly away from the waters
with this option, but perhaps that is another problem.

It's not a problem. That's what really happens. If you let the solvent to
follow a un-wrapped path, why do you think that it would be different for
your solute?  Unless you have a way to center the solute every frame.
So, IMHO, I think that this is not a problem.


My main question was though: can I stop mdrun from imaging all the
atoms before it outputs the original .xtc file? This is how Amber
does things by default, though of course there is no reason why
Gromacs should work this way - perhaps the coordinates are stored
internally in an imaged way?

Perhaps this should be answered by a developer ;)
But, I'm not aware of any flag inside the gmx pack that does that.
Is it really important that you produce un-wrapped trajectories? It's kind
of a cosmetic change, in order to see our solute surrounded by the solvent,
in a easy way.

On the other hand, I've already read somewhere a commentary about whether or
not writing a wrapped traj. could introduce some roundoff errors, that are
absent from an un-wrapped one.


Thanks

Dave

---- Message from "Nuno R. L. Ferreira" <nunolf at ci.uc.pt> at
2004-07-13 16:38:45 ------
>Hi David
>
>Check trjconv command. I think that -pbc flag has some value that
does that,
>a wrapp off.
>
>Best regards,
>Nuno
>
>######################################
>Nuno Ricardo Santos Loureiro da Silva Ferreira
>Departamento de Química
>Faculdade de Ciências e Tecnologia
>Universidade de Coimbra
>3004-535 Coimbra - Portugal
>Fax: +351 239 827703  - www.biolchem.qui.uc.pt
>########################################
>----- Original Message ----- 
>From: <david.evans at ulsop.ac.uk>
>To: <gmx-users at gromacs.org>
>Sent: Tuesday, July 13, 2004 4:25 PM
>Subject: [gmx-users] output unimaged trajectory?
>
>
>Dear all,
>
>Is it possible to get mdrun to output a trajectory where coordinates
>are not wrapped into the periodic box?
>I'm thinking of the default Amber behaviour (with IWRAP=0), if that
>helps anyone understand what I mean. I'm looking for maximum
>compatibility with Amber, and am also having problems getting trjconv
>to produce properly imaged trajectories.
>
>Thank you
>
>Dave Evans
>London School of Pharmacy
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